1. - Portfolio is in quick-start, so I do not understand the question
2. - If the menu is in a different position than the original it could mean for example that replaced the images with other dimensions

One second ...you're building website without quickstart? ...and on Joomla 2.5? why not on Joomla 3.0...? ok - do not matter ...
I understand that you want to have the menu below than it is now? like on demo?

Try to add a logo the same size as the original, not to scale logos give transparency. As this does not help you need to bury the "padding" or margins in the css files. Install yourself a debbuger (Mozilla's add-on) ... and there you can live preview css file changes...
At the slider I see the word "TEST" are you from Poland (Although the "test" is a universal word)

1000 times it is better to do something with Quickstart than without it. Without quickstart everything you need to manually turn on. When you have a quickstart you just changing a data! If you have a problem with installing quickstart I can do this it takes 20-30min. When I finish you change the password to the server...
I can you install quickstart in a subdirectory on the server you will see how much less work you will have...my email
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Unless you make a mistake as my friend once. Instead quickstart downloaded the template itself only (attachment d) :>

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